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- PDB-1r62: Crystal structure of the C-terminal Domain of the Two-Component S... -

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Basic information

Entry
Database: PDB / ID: 1r62
TitleCrystal structure of the C-terminal Domain of the Two-Component System Transmitter Protein NRII (NtrB)
ComponentsNitrogen regulation protein NR(II)
KeywordsTRANSFERASE / NRII / PII / HISTIDINE KINASE / TWO COMPONENT SYSTEM
Function / homology
Function and homology information


signal transduction => GO:0007165 / : / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / nitrogen fixation / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein autophosphorylation / hydrolase activity / regulation of DNA-templated transcription ...signal transduction => GO:0007165 / : / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / nitrogen fixation / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein autophosphorylation / hydrolase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / PAS fold ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensory histidine kinase/phosphatase NtrB / Sensory histidine kinase/phosphatase NtrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSong, Y. / Peisach, D. / Pioszak, A.A. / Xu, Z. / Ninfa, A.J.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of the C-terminal Domain of the Two-Component System Transmitter Protein Nitrogen Regulator II (NRII; NtrB), Regulator of Nitrogen Assimilation in Escherichia coli.
Authors: Song, Y. / Peisach, D. / Pioszak, A.A. / Xu, Z. / Ninfa, A.J.
History
DepositionOct 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulation protein NR(II)


Theoretical massNumber of molelcules
Total (without water)17,8441
Polymers17,8441
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.440, 32.940, 46.010
Angle α, β, γ (deg.)90.00, 108.19, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe full length NRII is a dimer, but the C-terminal domain is a monomer in solution

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Components

#1: Protein Nitrogen regulation protein NR(II)


Mass: 17844.275 Da / Num. of mol.: 1 / Fragment: C-terminal fragment (residues 190-349)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: NTRB / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P06712, UniProt: P0AFB5*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 5% PEG 20,000 and 0.1M MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 31, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 18060 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.05 % / Biso Wilson estimate: 0.249 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 35
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1705 / Rsym value: 0.198 / % possible all: 95.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→27.61 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1487105.04 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1742 9.9 %RANDOM
Rwork0.237 ---
all0.239 17649 --
obs0.239 15907 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.3315 Å2 / ksol: 0.411837 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20.31 Å2
2--1.92 Å20 Å2
3----0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 0 109 1182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 260 9.7 %
Rwork0.282 2413 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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